{ "_id": "6a104e5facfb0bcc41ca0a3a", "Package": "DTEBOP2", "Title": "Bayesian Optimal Phase II Randomized Clinical Trial Design with\nDelayed Outcomes", "Version": "1.0.3", "Authors@R": "c(\nperson(\"Zhongheng\", \"Cai\", email = \"zhonghengcai123@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Haitao\", \"Pan\", email = \"Haitao.Pan@STJUDE.ORG\", role = \"aut\")\n)", "Description": "Implements a Bayesian Optimal Phase II design (DTE-BOP2)\nfor trials with delayed treatment effects, particularly\nrelevant to immunotherapy studies where treatment benefits may\nemerge after a delay. The method builds upon the BOP2 framework\nand incorporates uncertainty in the delay timepoint through a\ntruncated gamma prior, informed by expert knowledge or default\nsettings. Supports two-arm trial designs with functionality for\nsample size determination, interim and final analyses, and\ncomprehensive simulation under various delay and design\nscenarios. Ensures rigorous type I and II error control while\nimproving trial efficiency and power when the delay effect is\npresent. A manuscript describing the methodology is under\ndevelopment and will be formally referenced upon publication.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "LazyData": "true", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-10 06:33:05 UTC", "User": "root" }, "Author": "Zhongheng Cai [aut, cre], Haitao Pan [aut]", "Maintainer": "Zhongheng Cai ", "Repository": "https://zhongheng-biostatistics.r-universe.dev", "Date/Publication": "2025-05-09 10:40:06 UTC", "RemoteUrl": "https://github.com/cran/DTEBOP2", "RemoteRef": "HEAD", "RemoteSha": "82a8d2be82a62dcad096a2bcfb2fb1af0f761d7e", "MD5sum": "52e1e9afe52eeb8d1f0b8444374e7d13", "_user": "zhongheng-biostatistics", "_type": "src", "_file": "DTEBOP2_1.0.3.tar.gz", "_fileid": "dd0bd6caeee377ddb3c072aa2d618726e3b2bdb5e664b59bb0259c8eda5deaba", "_filesize": 1162961, "_sha256": "dd0bd6caeee377ddb3c072aa2d618726e3b2bdb5e664b59bb0259c8eda5deaba", "_created": "2026-05-10T06:33:05.000Z", "_published": "2026-05-22T12:38:55.146Z", "_distro": "noble", "_jobs": [ { "job": 77380924740, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6901624726" }, { "job": 77380924640, "time": 134, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6901623763" }, { "job": 77380924644, "time": 164, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6901629572" }, { "job": 77380924659, "time": 171, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6901629337" }, { "job": 77380924223, "time": 356, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6901610856" }, { "job": 77380924239, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160659968" }, { "job": 77380924589, "time": 82, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6901619127" }, { "job": 77380924720, "time": 85, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6901619276" }, { "job": 77380924939, "time": 81, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6901618981" } ], "_buildurl": "https://github.com/r-universe/zhongheng-biostatistics/actions/runs/25621810947", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/DTEBOP2", "_commit": { "id": "82a8d2be82a62dcad096a2bcfb2fb1af0f761d7e", "author": "Zhongheng Cai ", "committer": "cran-robot ", "message": "version 1.0.3\n", "time": 1746787206 }, "_maintainer": { "name": "Zhongheng Cai", "email": "zhonghengcai123@gmail.com", "login": "zhongheng-biostatistics", "uuid": 182246117 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "truncdist", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "invgamma", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "survRM2adapt", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "reconstructKM", "role": "Suggests" }, { "package": "survival", "role": "Suggests" }, { "package": "survminer", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-19", "n": 1 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "zhongheng-biostatistics", "count": 1, "uuid": 182246117 } ], "_userbio": { "uuid": 182246117, "type": "user", "name": "zhongheng-Biostatistics" }, "_downloads": { "count": 569, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DTEBOP2" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DTEBOP2.html", "manual.pdf" ], "_realowner": "zhongheng-biostatistics", "_cranurl": false, "_releases": [ { "version": "1.0.3", "date": "2025-05-09" } ], "_exports": [ "conduct", "event_fun", "generate_pe", "get.optimal_2arm_piecewise", "getoc_2arm_piecewise", "rtrunc_gamma", "trunc_gamma_para", "TTOT_fun", "Two_stage_sample_size" ], "_datasets": [ { "name": "Experimental", "title": "Nivolumab KM data used for reconstructing PFS KM curve", "object": "Experimental", "class": [ "data.frame" ], "fields": [ "time", "survival" ], "rows": 48, "table": true, "tojson": true }, { "name": "SOC", "title": "Docetaxel KM data used for reconstructing PFS KM curve", "object": "SOC", "class": [ "data.frame" ], "fields": [ "time", "survival" ], "rows": 36, "table": true, "tojson": true } ], "_help": [ { "page": "conduct", "title": "Computes the hazard ratio between post- and pre-separation periods, provides the 95% Bayesian credible interval, and makes a Go/No-Go decision based on the trial data. This function is intended for interim and final analyses in two-arm survival trials with delayed treatment effects.", "topics": [ "conduct" ] }, { "page": "event_fun", "title": "Return expected event number at interim analysis and final analysis.", "topics": [ "event_fun" ] }, { "page": "Experimental", "title": "Nivolumab KM data used for reconstructing PFS KM curve", "topics": [ "Experimental" ] }, { "page": "generate_pe", "title": "Generate event times from a piecewise exponential distribution.", "topics": [ "generate_pe" ] }, { "page": "get.optimal_2arm_piecewise", "title": "Obtain Optimal Design Parameters for DTE-BOP2 Design", "topics": [ "get.optimal_2arm_piecewise" ] }, { "page": "getoc_2arm_piecewise", "title": "Compute Operating Characteristics for Two-Arm Piecewise Exponential Designs", "topics": [ "getoc_2arm_piecewise" ] }, { "page": "rtrunc_gamma", "title": "Generate Random Variables from a Truncated Gamma Distribution.", "topics": [ "rtrunc_gamma" ] }, { "page": "SOC", "title": "Docetaxel KM data used for reconstructing PFS KM curve", "topics": [ "SOC" ] }, { "page": "trunc_gamma_para", "title": "Estimate Shape and Scale Parameters for Truncated Gamma Distribution", "topics": [ "trunc_gamma_para" ] }, { "page": "TTOT_fun", "title": "Compute the Total Time-on-Test (TTOT) Statistic", "topics": [ "TTOT_fun" ] }, { "page": "Two_stage_sample_size", "title": "Calculate Sample Sizes for a Two-Stage Trial Design.", "topics": [ "Two_stage_sample_size" ] } ], "_rundeps": [ "codetools", "doParallel", "evd", "foreach", "invgamma", "iterators", "truncdist" ], "_vignettes": [ { "source": "DTEBOP2.Rmd", "filename": "DTEBOP2.html", "title": "DTEBOP2:An R Package for Designing Two-Arm Multi-Stage Survival Trials with Delayed Treatment Effects", "engine": "knitr::rmarkdown", "headings": [ "1. Introduction", "2. Eliciting the Truncated Gamma Prior for DTE Separation Timepoint ( S )", "3. Calculating Median Survival Times for Pre- and Post-Separation DTE Timepoint given DTE timepoint S", "4. Determination of Sample Size in a Two-Stage Design Setting", "5. Conduct the Trial: Make Go/No-Go Decision", "6. Summary", "7. Example 1", "8. Incorporating Early Stopping Probability into Sample Size Determination", "9. Application of the Proposed Method in a Three-Stage Design", "10. 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